Structural highlights
2j5r is a 4 chain structure with sequence from "flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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| Ligands: | |
| Related: | 1d3a, 1gt2, 1hlp, 1o6z, 2hlp, 2j5k, 2j5q |
| Activity: | Malate dehydrogenase, with EC number 1.1.1.37 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum |
Function
[MDH_HALMA] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.
Specific radiation damage to acidic residues and its relation to their chemical and structural environment.,Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M. Specific radiation damage to acidic residues and its relation to their chemical and structural environment. J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074 doi:10.1107/S0909049506038623
